WGS~genotyping-by-mpileup

genotyping by bcftools mpileup This pipeline is intended to analyze more than 100 samples and execute jobs in parallel.

input_1:paired-end FASTQ(.gz) files

input_1/DRR015801_10k_1.fastq

@DRR015801.1 HWI-ST895:156:C1HNFACXX:1:1101:2347:1967/1
NACATCATCACATCGCTGGGCTGTCTGGAAGGTGGTGACCTGGATATCGCTTATCTTTCTGAAATTGACCCCACCTGGACGGACAGCAGCCTGACCACCA
+
#1:DDDFFHGHHHJJIJJBHIJJIHIJJJIJJ?DGDHIJJJIJIJJJJJJJJJJJJJJJIJIIJHHHHHHFFFDDCEDDDDDDDDDDDDDDDDDDDDDDD
@DRR015801.2 HWI-ST895:156:C1HNFACXX:1:1101:2281:1982/1
NTATCTTGCTATCCCCAAAAAATTCAGAGATGAGTCGAAAGTCATATCTTTCATGTATGATAAGAATAAAACGTATATTTTGCTATTTTTGATTGCTTTT
+
#1=DDFFFHHHHHJJJJJJJJJJJJJJJIIJJIIHIIJIJJEHIJJJIJJJIJJJGIJJJJJIJIJJJJJHHHHFBFFFFEEEEEEEEDD@DDDDDDDDC
@DRR015801.3 HWI-ST895:156:C1HNFACXX:1:1101:2751:1963/1
NAGAAACCTCCTGAGATCACCCTGAAAAGAATAGGAGAGGAGGCGGGTAAAATCTATATGATACAGAGACAACGATGTTCCCGCTGTGGGACACAGCGGG

input_1/DRR015801_10k_2.fastq

@DRR015801.1 HWI-ST895:156:C1HNFACXX:1:1101:2347:1967/2
GCATATTAAAGGCGCTGGCAATGGCATCTGCTGCACAGGCCCCCTGTGCTATCGGATTGGCAAAGATGACAGCTTCCGGATTGAGAATGGTGGTCAGGCT
+
CCCFFFFFHHHGGJIJIJJJJIJJJJIJJIICGGJJIGIJJJIJHIHIIGFGGIJGHHCDEFFECCCECEDCACDDDDDBBB<ACBDDCC4@B5CCDDD@
@DRR015801.2 HWI-ST895:156:C1HNFACXX:1:1101:2281:1982/2
GTGTATGGGCAAATGAAACCATTGAAAAAGCAATCAAAAATAGCAAAATATACGTTTTATTCTTATCATACATGAAAGATATGACTTTCGACTCATCTCT
+
@BCDFFFFHHHHHJJJJJJJJJJIJGJIHGHIJJJJJJJJIJIJJJJIJJHIIIGIJJIJJIJJIIJJJIJJJIHHHHHFFFFFFFFEEDDDDDDDDDDE
@DRR015801.3 HWI-ST895:156:C1HNFACXX:1:1101:2751:1963/2
CAGTCGATCAATAATATTCCACTGGATGCGCGTAATCACGGCTATACGGTGCTGGATATTCAGCAAGACGGGCCGACCATTCGTTATTTAATTCAGAAAT

input_2:reference genome file

input_2/ecoli.fasta

>ecoli
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT

Option

input_1/ input_2/ecoli.fasta

Output

all.vcf

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##bcftoolsVersion=1.9+htslib-1.9
##bcftoolsCommand=mpileup -Ou --annotate AD,DP,INFO/AD -r ecoli -f input_2/ecoli.fasta output.bwa/DRR015801_10k.bam
##reference=file://input_2/ecoli.fasta
##contig=<ID=ecoli,length=4641652>
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">

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